[Ifeffit] XAFS Analysis using Ifeffit
Francois.Farges at univ-mlv.fr
Sat Jul 29 03:06:27 CDT 2006
to mam : your referee is a dumb, clearly ! feff8 can do both. One more
quick and dirty referee. Some journals do money nowadays. Easy to answer
there is an EXAFS card, which is not made for XANES, clearly...
to all : gnxas is not designed to be easy to use; it is not designed as a
"black box". it needs some effort and that's an opposite way to feff.
this strategy has its own pros and cons; and corresponds to what was
taught in Italy and France in the 90's on XAFS ("work hard school"). I
survived it ...
But the authors have considerably modified they vision recently (open to
actinides) and it is becoming more more accessible, tough not as easy as
feff. For instance, the great biotech group at SSRL widely use it.
One advantage of their strategy is that not everyone can claim to do
"state of the art" EXAFS simulation without some deep understanding of
what's going on. I've seen, in contrast, papers in which people were
claiming so much about feff (so-call "good and bad things") but their
calculations were far from optimum (they are never, I know for sure myself
!) so their feff "evaluation" was quite very poor in fact.
also gnxas is not just for glasses. it is for everything of course. they
applied it often to glasses because it corresponds to what physicists
where highly interested in the 90's. Nowadays the situation is quite
different because environmental and biological sciences invaded the field
but gnxas is highly involved in the biotech field at SSRL, for instance.
With gnxas, this is not to happen soon because you always feel to be a
"primitive and modest gnxas user", given the intrinsic complexity of the
program and its numerous options and, I must say, its documentation that
is not always updated as the code is; leaving some perplexity, if not bad
Also, the graphical subroutine uses some kind of unpopular primitive odd
(dumb) library that is not always very easy to find or to install (many
alternatives would be much more easier ...)
Finally, their supported plateforms is not typical of what users now use
nowadays. Surprisingly, they promote either very expensive proprietary (HP
UNIX, VMS etc) or so-calmled "open source" free plateforms (Linux)(Red Hat
is no more but a gnxas distribution for RedHat is still available; so
there is some inconsistencies here in the gnxas policies). That's their
choice but it is getting more and more 90's outdated, not reflecting 2006.
But basically, a modernized front end of gnxas would be great. But one has
to get into that programming to make it easy-to-click (like many would
like too). With Atoms of Bruce Ravel, there are options to prepare these
so-odd files needed for gnxas. this is already a wonderful first step.
Any decent model of the EXAFS for high Z cations should be done with that
program, basically. Sixpack, ifeffit, but mostly FEFF, are missing the
multi-electronic excitation (MEE) modeling. This is well known and their
authors are well aware of this limitation. The atomic-XAFS vs. MEE
"battle" a few years ago contributed to this unfortunate segmentation.
But most users don't even "smell" these MEE's (or AXAFS if you prefer) in
their data and process them straight away. they cannnot be 100% blamed,
MEE are also quite vicious features. but more and more is done that is not
appropriate because of these nice GIUs (athena, sixpack). so it is
difficult to decide what to do.
Also, like others, I ve found that MEE are more and more visible as much
as the metal concentration probed is getting lower and lower (comparative
study of Mn permanganate solutions at more and more dilutions makes that
the MEE is increadingly more detected in the normalized EXAFS). And this
now standard to look at diluted metals, in environmental samples with
these 3rd generation, highly-stabilized sources (SLS for instance).
But we are getting more or less overflowded with data with all these new
sources everywhere and funding agencies need papers and we go straight
MAM : I won't blame them not to have Windows version as I know many other
GREAT programs, incl. yours, that run only on Windows (still, what a
limitation to be better quoted...) as they could easily run on other
plateforms... (get rid of these registers !). I'm thinking also to the
So, any close future to get more gnxas done, if one does not want to jump
into it... and still the best exafs-fitting package for sure. We all wish
to be using it more but this is not gonna happen soon.
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